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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.25

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-22, 14:29 EST based on data in:


        Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

        General Statistics

        Showing 0/81 rows and 4/6 columns.
        Sample NameDupsGCAvg lenMedian lenFailedSeqs
        NAO-ONT-20241025-Zephyr4-01-div0001
        30.3%
        42.0%
        320bp
        124bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-01-div0002
        32.8%
        38.0%
        340bp
        174bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-01-div0003
        34.5%
        36.0%
        316bp
        149bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-01-div0004
        34.1%
        37.0%
        409bp
        249bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-01-div0005
        37.3%
        38.0%
        342bp
        149bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-01-div0006
        33.5%
        35.0%
        305bp
        174bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-01-div0007
        29.8%
        38.0%
        304bp
        174bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-02-div0001
        45.4%
        46.0%
        176bp
        49bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-02-div0002
        38.2%
        49.0%
        250bp
        49bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-02-div0003
        31.4%
        50.0%
        215bp
        74bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-02-div0004
        40.4%
        47.0%
        221bp
        74bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-02-div0005
        37.9%
        49.0%
        183bp
        74bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-02-div0006
        37.2%
        47.0%
        156bp
        74bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-02-div0007
        33.3%
        49.0%
        170bp
        74bp
        30%
        0.0M
        NAO-ONT-20241025-Zephyr4-03-div0001
        27.5%
        48.0%
        120bp
        49bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-03-div0002
        24.3%
        51.0%
        146bp
        49bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-03-div0003
        22.5%
        52.0%
        161bp
        24bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-03-div0004
        22.2%
        47.0%
        170bp
        49bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-03-div0005
        20.0%
        53.0%
        120bp
        24bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-03-div0006
        16.4%
        54.0%
        127bp
        24bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-03-div0007
        16.0%
        54.0%
        144bp
        24bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-04-div0001
        54.7%
        48.0%
        121bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-04-div0002
        51.9%
        49.0%
        146bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-04-div0003
        47.4%
        49.0%
        201bp
        99bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-04-div0004
        44.1%
        48.0%
        171bp
        74bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-04-div0005
        50.5%
        48.0%
        147bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-04-div0006
        47.8%
        48.0%
        222bp
        99bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-04-div0007
        47.9%
        49.0%
        130bp
        74bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-05-div0001
        42.6%
        40.0%
        3661bp
        2999bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-05-div0002
        44.8%
        39.0%
        3610bp
        3499bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-05-div0003
        44.8%
        39.0%
        3486bp
        3749bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-05-div0004
        43.9%
        39.0%
        3394bp
        3749bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-05-div0005
        43.2%
        39.0%
        3477bp
        3499bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-05-div0006
        42.3%
        39.0%
        3423bp
        3749bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-05-div0007
        29.0%
        39.0%
        3600bp
        3899bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-06-div0001
        45.2%
        42.0%
        573bp
        499bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-06-div0002
        43.9%
        38.0%
        87bp
        49bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-06-div0003
        44.3%
        43.0%
        49bp
        52bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-06-div0004
        38.7%
        42.0%
        53bp
        52bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-06-div0005
        48.0%
        37.0%
        54bp
        49bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-06-div0006
        42.9%
        37.0%
        140bp
        99bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-06-div0007
        42.9%
        44.0%
        51bp
        52bp
        30%
        0.0M
        NAO-ONT-20241025-Zephyr4-07-div0001
        48.3%
        14.0%
        119bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-07-div0002
        48.5%
        12.0%
        121bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-07-div0003
        52.8%
        17.0%
        523bp
        499bp
        70%
        0.0M
        NAO-ONT-20241025-Zephyr4-07-div0004
        52.1%
        11.0%
        163bp
        99bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-07-div0005
        53.6%
        9.0%
        132bp
        74bp
        70%
        0.0M
        NAO-ONT-20241025-Zephyr4-07-div0006
        49.9%
        10.0%
        131bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-07-div0007
        43.0%
        27.0%
        297bp
        249bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-08-div0001
        42.6%
        32.0%
        68bp
        49bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-08-div0002
        36.9%
        34.0%
        70bp
        54bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-08-div0003
        41.2%
        30.0%
        104bp
        74bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-08-div0004
        27.8%
        35.0%
        73bp
        54bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-08-div0005
        47.6%
        33.0%
        139bp
        49bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-08-div0006
        30.4%
        22.0%
        124bp
        74bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-08-div0007
        35.6%
        33.0%
        80bp
        49bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-09-div0001
        43.3%
        29.0%
        109bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-09-div0002
        42.2%
        26.0%
        107bp
        69bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-09-div0003
        40.5%
        24.0%
        140bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-09-div0004
        46.0%
        22.0%
        157bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-09-div0005
        39.2%
        26.0%
        132bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-09-div0006
        47.2%
        24.0%
        154bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-09-div0007
        30.7%
        33.0%
        143bp
        74bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-10-div0001
        43.0%
        36.0%
        1041bp
        99bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-10-div0002
        47.2%
        36.0%
        1030bp
        249bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-10-div0003
        50.2%
        36.0%
        2564bp
        2499bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-10-div0004
        52.1%
        35.0%
        762bp
        99bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-10-div0005
        50.1%
        35.0%
        836bp
        99bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-10-div0006
        49.8%
        35.0%
        910bp
        249bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-10-div0007
        33.1%
        36.0%
        1208bp
        99bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-11-div0001
        49.9%
        33.0%
        73bp
        24bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-11-div0002
        46.9%
        39.0%
        66bp
        74bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-11-div0003
        44.2%
        42.0%
        51bp
        49bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-11-div0004
        54.3%
        33.0%
        82bp
        24bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-11-div0005
        50.6%
        41.0%
        45bp
        44bp
        60%
        0.0M
        NAO-ONT-20241025-Zephyr4-11-div0006
        42.9%
        41.0%
        63bp
        24bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-11-div0007
        44.7%
        36.0%
        57bp
        49bp
        50%
        0.0M
        NAO-ONT-20241025-Zephyr4-13-div0003
        0.0%
        35.0%
        5066bp
        5066bp
        30%
        0.0M
        NAO-ONT-20241025-Zephyr4-15-div0006
        0.0%
        43.0%
        102bp
        102bp
        40%
        0.0M
        NAO-ONT-20241025-Zephyr4-18-div0005
        0.0%
        49.0%
        2764bp
        2764bp
        30%
        0.0M
        NAO-ONT-20241025-Zephyr4-unclassified
        40.6%
        28.0%
        10448bp
        9999bp
        60%
        0.0M

        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        T
        68
        941
        0.7804%
        C
        65
        1272
        1.0548%
        G
        64
        1439
        1.1933%
        AGATCATTGCTGTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGT
        61
        1223
        1.0142%
        A
        59
        406
        0.3367%
        AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
        53
        12092
        10.0277%
        AGATCATTGCCGTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGT
        48
        176
        0.1460%
        TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
        46
        2067
        1.7141%
        AGATCTTGCTGTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTG
        44
        117
        0.0970%
        AGATCATTGCTGTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTGGT
        42
        104
        0.0862%
        AGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
        40
        3763
        3.1206%
        AGATATTGCTGTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTG
        36
        69
        0.0572%
        ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
        35
        866
        0.7182%
        AGATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
        35
        357
        0.2961%
        ACCAGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCT
        34
        220
        0.1824%
        GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
        27
        195
        0.1617%
        AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
        26
        1940
        1.6088%
        AGATCATTGCTGTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCAT
        25
        36
        0.0299%
        AGATCATTGCTGTTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCG
        24
        32
        0.0265%
        AATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
        23
        194
        0.1609%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1